Chromatin Remodeling Complex SWR1 Regulates Root Development by Affecting the Accumulation of Reactive Oxygen Species (ROS)
Round 1
Reviewer 1 Report
Huang and colleagues present the role of SWR1 complex in ROS metabolism for root development. They employ mutants of SWR1 complex components arp6 and pie1 and triple mutants of H2A.Z genes to investigate the root phenotypes and molecular mechanisms in gene expression and epigenetic modification.
They find that root length and lateral root formation are affected in the above mutants. Transcriptomic analyses uncover the deduction of genes related to ROS metabolism such as MSRB6, APX4… in mutants. Moreover, they discover the corresponding ROS accumulation defects in the root of mutants. Furthermore, they investigate the epigenetic enrichments including H2A.Z, Pol II, H3K4me3, and H3K27me3 in the promoter regions of ROS related genes and find that active markers (H2A.Z, Pol II and H3K4me3) are significantly decreased. In contrast, the repressive marker (H3K27me3) is increased. Therefore, they propose an epigenetic regulation of SWRI in ROS metabolism and root development.
This manuscript integrates transcriptomic analyses, epigenetic approaches, and phenotypic investigation, and highlights the importance of epigenetic regulation in root development mediated by SWR1 complex and H2A.Z deposition. The story is interesting and could attract some interest in root development and epigenetic research. The manuscript is well-organized. The results are convincing and clear. I have some comments to help the authors to improve the manuscript better.
Comments:
1. Writing needs to be improved. For example, in Lines 15-16, a verb is missed in the first sentence in Abstract or “which” should be removed; in line 32, “the functions of” should be removed; in line 33, is “highlights” the verb of “our results” or “SWR1”? Overall, writing must be revised carefully.
2. Lines 21-22, “the mutants for the components of Arabidopsis SWR1….hta8 hta9 hta11 triple mutant”. This statement is confusing. Based on the introduction, H2A.Z is reasonably associated with SWR1 as SWR1 could catalyze the replacement of H2A with H2A.Z, however, H2A.Z is not a component of SWR1 complex.
3. Figure 1 B, C, E, and G, the statistical analyses should be done and shown in box-plots.
4. Figure 5 G and E, why do they analyze the H2A.Z deposition in AT4G07700 and HSP70-1? As they show six genes in all other analyses, it makes me curious why they show the extra two genes in this H2A.Z analysis.
Author Response
Reviewer 1:
Point 1: Writing needs to be improved. For example, in Lines 15-16, a verb is missed in the first sentence in Abstract or “which” should be removed; in line 32, “the functions of” should be removed; in line 33, is “highlights” the verb of “our results” or “SWR1”? Overall, writing must be revised carefully.
Response 1: We are very sorry for these mistakes in the manuscript. In the revised version, we revised the relevant sentences carefully and invited a professional English editor to review the writing.
Point 2: Lines 21-22, “the mutants for the components of Arabidopsis SWR1….hta8 hta9 hta11 triple mutant”. This statement is confusing. Based on the introduction, H2A.Z is reasonably associated with SWR1 as SWR1 could catalyze the replacement of H2A with H2A.Z, however, H2A.Z is not a component of SWR1 complex.
Response 2: We are very sorry for this mistake in the manuscript, and we have revised this sentence in the revised version.
Point 3: Figure 1 B, C, E, and G, the statistical analyses should be done and shown in box-plots.
Response 3: Thank you for your suggestion. We have revised these figures in the revised version.
Point 4: Figure 5 G and E, why do they analyze the H2A.Z deposition in AT4G07700 and HSP70-1? As they show six genes in all other analyses, it makes me curious why they show the extra two genes in this H2A.Z analysis.
Response 4: Thank you for your pointing out. We removed these Figure 5 G and E in the revised version.
Reviewer 2 Report
Dear Authors,
I reviewed your article titled (Chromatin remodeling complex SWR1 regulates root develop mint via affecting the accumulation of reactive oxygen species (ROS). Overall, the data presented here is highly valuable to those working in this field and demonstrates the effectiveness of a relatively simple intervention that could be applied on a wider scale, especially in the field of genetic engineering. The article is written very well and organized. It is difficult to find any mistakes. However, there are some minor comments that could be useful to improve the quality of your article, which I have specified below and also mentioned in the attached pdf file:
Abstract and Introduction:
The abstract and introduction are written well and have enough literature related to the subject. Some minor comments here:
1- Line 20: GO analysis: Please start with the full name and then continue with the abbreviation. Revised the whole MS.
2- line 35: use words different than the title and arrange the words alphabetically.
Result and Discussion
This section overall is very well written. The language is clear, concise, and sufficiently descriptive with a logical flow between statements. Some comments:
1- Figure 2: The data presented in sub-fig c and d are unclear. Please make words more visible.
2- Figure 3 and 4: Please add the significant letters.
3- Line 292: Use the abbreviation
Materials and methods:
All methods are enough described. The design of the experiment is correct. Some minor comments are:
1- Line 387: the statistical analysis method is missing. Please add this section before the conclusion.
Comments for author File: 
Comments.pdf
Author Response
Reviewer 2
Abstract and Introduction:
The abstract and introduction are written well and have enough literature related to the subject. Some minor comments here:
Point 1: Line 20: GO analysis: Please start with the full name and then continue with the abbreviation. Revised the whole MS.
Response 1: Thank you for your suggestion. We have revised the related sentences in the revised version.
Point 2: line 35: use words different than the title and arrange the words alphabetically.
Response: Thank you for your suggestion. We revised the order of keywords in the revised version.
Result and Discussion
This section overall is very well written. The language is clear, concise, and sufficiently descriptive with a logical flow between statements. Some comments:
Point 3: Figure 2: The data presented in sub-fig c and d are unclear. Please make words more visible.
Response 3: Thank you for your suggestion. We have revised these figures in the revised version.
Point 4: Figure 3 and 4: Please add the significant letters.
Response 4: Thank you for your suggestion. We have revised these figures in the revised version.
Point 5: Line 292: Use the abbreviation
Response 5: Thank you for your suggestion. We have revised the related sentence in the revised version (Line 280).
Materials and methods:
All methods are enough described. The design of the experiment is correct. Some minor comments are:
Point 6: Line 387: the statistical analysis method is missing. Please add this section before the conclusion.
Response 6: Thank you for your suggestion. In the revised version, we have added the statistical analysis method in the “Materials and methods” section (Line 384-388).
Reviewer 3 Report
The manuscript by Huang etal describes the role of several components of SWR1 complex in root growth and the effect on ROS metabolism. The results are interesting and highlight the role of the deposition of H2A.Z in the chromatin during root growth.
The results could be improved.
a) Need to revise the English in several cases. Some examples in the abstract are the following
-a type of oxygen monoelectronic reduction product, which play integral roles in root growth and development. Delete "which".
-Epigenetic mechanism plays a critical role in regulating gene transcription and expression. Delete "regulating".
-Transcriptome results and GO analysis showed that the oxidoreductase activity related genes were significantly changes in mutants. Replace "were significantly changes" with "significantly changed".
-ROS in the mutants of SWR1 complex were caused by the reduced H2A.Z deposition in oxidoreductase activity related genes. Add "the SWR1", REPLACE were with was.
In figure 1. B, C, E, and G require statistical analysis. Please provided.
In figure 5, 6, 7, 8 the authors need to present the data as a ratio against H3 antibody.
Finally, in figure 4, please provide how they measure the intensity.
Author Response
Reviewer 3
The manuscript by Huang etal describes the role of several components of SWR1 complex in root growth and the effect on ROS metabolism. The results are interesting and highlight the role of the deposition of H2A.Z in the chromatin during root growth. The results could be improved.
Point 1: Need to revise the English in several cases. Some examples in the abstract are the following
-a type of oxygen monoelectronic reduction product, which play integral roles in root growth and development. Delete "which".
-Epigenetic mechanism plays a critical role in regulating gene transcription and expression. Delete "regulating".
-Transcriptome results and GO analysis showed that the oxidoreductase activity related genes were significantly changes in mutants. Replace "were significantly changes" with "significantly changed".
-ROS in the mutants of SWR1 complex were caused by the reduced H2A.Z deposition in oxidoreductase activity related genes. Add "the SWR1", REPLACE were with was.
Response 1: We are very sorry for these mistakes in the manuscript. In the revised version, , we revised the relevant sentences carefully and invited a professional English editor to review the writing.
Point 2: In figure 1. B, C, E, and G require statistical analysis. Please provided.
Response 2: Thank you for your suggestion. In the revised version, we revised the Figure 1. B, C, E based on another Reviewer's suggestion, and we also explain the statistical analysis method in the Figure legends and “Materials and methods” section (Line 112-129, Line 384-388).
Point 3: In figure 5, 6, 7, 8 the authors need to present the data as a ratio against H3 antibody.
Response 3: Thank you for your suggestion. We performed the ChIP-qPCR experiment using H3 antibody and present the data as a ratio against H3 antibody in the Figure 5, 6, 7, 8. We have revised these figures in the revised version.
Point 4: Finally, in figure 4, please provide how they measure the intensity.
Response 4: Thank you for your suggestion. In the revised version, we have explained this method in the “Materials and methods” section (Line 381-383).
Round 2
Reviewer 3 Report
The authors made most of my suggestions. Therefore, the manuscript is publishable!
